The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages

Abstract

Diverse CRISPR-Cas systems constitute an indispensable part of the bacterial adaptive immune system against viral infections. However, to escape from this immune system, bacteriophages have also evolved corresponding anti-defense measures. We investigated the diversity of CRISPR-Cas systems and the presence of prophages in the genomes of 66 Bifidobacterium pseudocatenulatum strains. Our findings revealed a high occurrence of complete CRISPR-Cas systems (62%, 41/66) in the B. pseudocatenulatum genomes. Subtypes I-C, I-U and II-A, were found to be widespread in this species. No significant association was found between the number of bacterial CRISPR spacers and its host's age. This study on prophages within B. pseudocatenulatum genomes revealed that prophage genes related to distinct functional modules became degraded at different levels, indicating that these prophages were not likely to enter lytic cycle spontaneously. Further, the evolutionary analysis of prophages in this study revealed that they might be derived from different phage ancestors. Notably, self-targeting phenomenon within B. pseudocatenulatum and Anti-CRISPR (Acr) coding genes in prophages was observed. Overall, our results indicate that the competition between B. pseudocatenulatum and phages is a major driving factor for the genomic diversity of both partners.

Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity

“…Genome sequencing and comparative genomics of seven newly sequenced and 50 publicly available E. lenta isolates allowed us to establish that 5.6% of the orthologous groups (OGs) that form the pangenome of E. lenta can be associated with prophages. This value is within range for prophages infecting other species of Actinobacteria, estimated at between 2% to 6.7% of OGs forming the Bifidobacterium pangenome [77,93].…”

“…These observations may explain the lack of an obvious correlation between the presence or absence of a CRISPR/cas system and the number of prophages associated with a host genome. As has been determined for other Actinobacteria genera such as Bifidobacterium, the presence of CRISPR/cas does not mean a bacterium genome will possess fewer prophage elements in its genome [93].…”

Microbial-Induced Carbonate Precipitation Improves Physical and Structural Properties of Nanjing Ancient City Walls

“…Moreover, the pores near the surface are more effectively sealed by MICP than the deeper pores in the brick cubes as revealed by X-ray micro-CT. Chen et al [33] and Sun et al [34] also demonstrated that the internal concrete cracks could not be repaired as well as the cracks near the surface. One possible reason could be that the fluidity of the MICP medium is relatively low likely due to the silica powder mixed into the slurry [10]. MICP with pure liquid media can directly repair cracks with a width less than 0.4 mm, while for wider cracks, it is necessary to use fine sand, silica powder, and/or other fillers [35].…”

“…They can adsorb Ca 2+ from the solution as crystallization nuclei, producing microbial-induced calcite bridges on the adjacent particles to form cemented bio-calcareous rock [8]. Inspired by the natural ability of MICP, researchers have used this technique as a promising self-healing technology for concrete crack remediation and improvement of ash bricks [9,10]. Therefore, MICP could also be a biological control tool against the cracks of city wall bricks as well as for other ancient remnants subjected to deterioration from uncontrolled cracking.…”

Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System

“…For instance, bacterial numbers are estimated at 10 11 cells per gram weight of fecal material compared to approximately 10 12 bacteriophages in the same amount ( Cani, 2018 ). Bacteriophages have been shown to drive the composition of the gut microbiome ( Moreno-Gallego et al, 2019 ) by specifically targeting gut bacteria and creating an evolutionary arms race between bacterial host and virus ( Azam and Tanji, 2019 ; Wang G. et al, 2020 ). Further, studies have shown the capacity of bacteriophages to disrupt biofilms ( Hansen et al, 2019 ; Lusiak-Szelachowska et al, 2020 ), kill intracellular bacteria ( Jonczyk-Matysiak et al, 2015 ), and modulate the immune system ( Van Belleghem et al, 2018 ), all key to counteracting virulence mechanisms that oncobacteria use to promote tumor growth ( Holt and Cochrane, 2017 ).…”